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Ioannis Xenarios

Group Leader Swiss-Prot and Vital-IT. E-mail: ioannis.xenarios@isb-sib.ch SIB Swiss Institute of Bioinformatics Quartier Sorge-Batiment Genopode CH-1015 Lausanne Switzerland Phone: +41 (0)21 692 4031 Fax: +41 (0)21 692 4065 SIB Swiss Institute of Bioinformatics CMU, Rue Michel Servet, 1 CH-1211 Geneva Switzerland Phone: +41 (0)22 379 4172 Fax: +41 (0)22 379 5858

Short biography

Dr. Ioannis Xenarios has a PhD in immunology from the Ludwig Institute of Cancer Research and the Institute of Biochemistry of the University of Lausanne, and is since 2010 full professor at the University of Lausanne (UNIL). Dr. Xenarios' expertise has been built around viruses and host interactions. During his postdoctoral fellowship he created under the guidance of Professor David Eisenberg at the University of California Los Angeles (UCLA) the first protein-protein interactions database (DIP), one of the three major interaction databases in the world. Dr. Xenarios led several groups in the Merck-Serono Pharmaceutical Research Institute, centered on computational methodologies development in the fields of proteomics, genomics and genetics. His research activities are at the interface of gene regulatory network modeling and computational biology. He is one of the 15 members of the Scientific Committee for the Innovative Medicine Initiative, and involved in the Proteomics Standard Initiative (PSI-MI). Dr. Xenarios leads the Vital-IT group at the SIB Swiss Institute of Bioinformatics in Lausanne, as well as the Swiss-Prot group at SIB in Geneva.

Groups

The Vital-IT group is an innovative life science informatics initiative providing computational resources, consultancy and training to connect fundamental and applied research. It is a collaboration between the SIB, the Universities of Lausanne and Geneva, the Ludwig Institute for Cancer Research, the Swiss Federal Institute of Technology Lausanne (EPFL), and industrial partners. Vital-IT also provides a web server offering access to a range of databases, software tools and services. Vital-IT helps to support postgraduate education through training sessions and workshops in a coordinated manner with several SIB and institutional partners.

The Swiss-Prot group develops, annotates and maintains the UniProtKB/Swiss-Prot protein sequence database, and also other databases including PROSITE, a database of protein families and domains, and ENZYME, a database of enzyme nomenclature. The group also co-heads the development and maintenance of the ExPASy proteomics website, a life sciences portal which serves as an entry point to several databases and to various online bioinformatics tools.

Selected publications

  1. Hulo C, de Castro E, Masson P, Bougueleret L, Bairoch A, Xenarios I, Le Mercier P: ViralZone: a knowledge resource to understand virus diversity. Nucleic Acids Res., 2011, 39: D576-82.
  2. UniProt Consortium: Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res., 2011, 39: D214-9.
  3. Wurm Y, Wang J, Riba-Grognuz O, Corona M, Nygaard S, Hunt BG, Ingram KK, Falquet L, Nipitwattanaphon M, Gotzek D, Dijkstra MB, Oettler J, Comtesse F, Shih CJ, Wu WJ, Yang CC, Thomas J, Beaudoing E, Pradervand S, Flegel V, Cook ED, Fabbretti R, Stockinger H, Long L, Farmerie WG, Oakey J, Boomsma JJ, Pamilo P, Yi SV, Heinze J, Goodisman MA, Farinelli L, Harshman K, Hulo N, Cerutti L, Xenarios I, Shoemaker D, Keller L: The genome of the fire ant Solenopsis invicta. Proc. Natl. Acad. Sci. U S A, 2011, Jan 31 (Epub ahead of print).
  4. Gene Ontology Consortium: The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res., 2010, 38: D331-5.
  5. Liechti R, Csardi G, Bergmann S, Sch?tz F, Sengstag T, Boj SF, Servitja JM, Ferrer J, Van Lommel L, Schuit F, Klinger S, Thorens B, Naamane N, Eizirik DL, Marselli L, Bugliani M, Marchetti P, Lucas S, Holm C, Jongeneel CV, Xenarios I: EuroDia: a beta-cell gene expression resource. Database (Oxford), 2010:baq024.
  6. Liechti R, Gleizes A, Kuznetsov D, Bougueleret L, Le Mercier P, Bairoch A, Xenarios I: OpenFluDB, a database for human and animal influenza virus. Database (Oxford), 2010:baq004.
  7. Santuari L, Pradervand S, Amiguet-Vercher AM, Thomas J, Dorcey E, Harshman K, Xenarios I, Juenger TE, Hardtke CS: Substantial deletion overlap among divergent Arabidopsis genomes revealed by intersection of short reads and tiling arrays. Genome Biol., 2010, 11: R4.
  8. Schuepbach T, Xenarios I, Bergmann S, Kapur K: FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinformatics, 2010, 26: 1468-9.
  9. Abhishek G, Mohanram K, Di Cara A, De Micheli G, Xenarios I: Modeling Stochasticity and Robustness in Gene Regulatory Networks. Bioinformatics 2009, 25: i101-9.
  10. Gattiker A, Dessimoz C, Xenarios I, Pagni M, Rougemont J: The Microbe browser for comparative genomics. Nucleic Acid Res., 2009, 37: W296-9.
  11. Kahlem P, Clegg A, Reisinger F, Xenarios I, Hermjakob H, Orengo C, Birney E: ENFIN?A European network for integrative systems biology. C R Biol., 2009, 332: 1050-8.
  12. Rougemont J, Amzallag A, Iseli C, Farinelli L, Xenarios I, Naef F: Probabilistic base calling of Solexa sequencing data. BMC Bioinformatics, 2008, 9: 431.
  13. Taylor CF, Binz PA, Aebersold R, Affolter M, Barkovich R, Deutsch EW, Horn DM, H?hmer A, Kussmann M, Lilley K, Macht M, Mann M, M?ller D, Neubert TA, Nickson J, Patterson SD, Raso R, Resing K, Seymour SL, Tsugita A, Xenarios I, Zeng R, Julian RK Jr: Guidelines for reporting the use of mass spectrometry in proteomics. Nat. Biotechnol., 2008, 26: 860-1.
  14. Di Cara A, Garg A, De Micheli G, Xenarios I, Mendoza L: Dynamic simulation of regulatory networks using SQUAD BMC. Bioinformatics, 2007, 8: 462.
  15. Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H: Broadening the Horizon ? Level 2.5 of the HUPO-PSI Format for Molecular Interactions. BMC Biol., 2007, 5: 44.